Contacts of the strand formed by residues 241 - 250 (chain A) in PDB entry 6GE3


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with THR 241 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  GLN*     3.6     0.2    -      -       -      -
    237A  GLN*     2.9    56.7    +      -       +      +
    238A  ASP*     2.7    40.3    +      -       -      +
    239A  PRO      3.6     0.2    -      -       -      -
    240A  ASP*     1.3    81.2    +      -       -      +
    242A  TYR*     1.3    69.2    +      -       -      +
    243A  ASN*     4.8     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  GLU*     3.8    37.2    -      -       +      +
    235A  GLN      3.4     4.5    -      -       -      +
    236A  GLN*     3.4    51.4    +      -       +      -
    239A  PRO      3.7    20.3    +      -       -      -
    240A  ASP*     4.3     4.0    +      -       -      -
    241A  THR*     1.3    83.3    -      -       -      +
    243A  ASN*     1.3    67.5    +      -       -      +
    244A  LYS*     4.1     1.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  LEU      3.6     2.1    -      -       -      +
    234A  GLU*     3.4     2.6    -      -       -      -
    235A  GLN*     2.7    51.3    +      -       +      +
    237A  GLN*     3.1    34.7    +      -       -      +
    241A  THR*     4.8     4.8    -      -       -      +
    242A  TYR*     1.3    78.2    -      -       -      +
    244A  LYS*     1.3    59.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  PHE*     3.7    43.6    -      -       +      -
    233A  LEU      3.4     4.7    -      -       -      +
    234A  GLU*     4.3    15.9    -      -       +      +
    242A  TYR*     4.1     2.5    +      -       +      +
    243A  ASN*     1.3    73.6    -      -       -      +
    245A  HIS*     1.3    61.3    +      -       -      +
    246A  LEU*     3.8    27.3    +      -       +      +
    363A  ARG*     5.1     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 245 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  PHE*     3.2     4.3    -      -       -      +
    233A  LEU*     2.8    40.6    +      -       +      +
    243A  ASN      4.2     0.6    +      -       -      -
    244A  LYS*     1.3    73.6    -      -       -      +
    246A  LEU*     1.3    74.2    +      -       -      +
    247A  PHE*     3.9     9.2    -      +       -      -
    301A  ASP*     2.7    57.6    +      -       -      -
    303A  ASN      3.3    19.5    +      -       -      -
    304A  THR*     3.5    36.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 246 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  SER*     4.6    13.2    -      -       -      +
    231A  ALA      3.7     5.2    -      -       -      +
    232A  PHE*     3.7    21.3    -      -       +      -
    244A  LYS*     3.8    22.4    +      -       +      +
    245A  HIS*     1.3    89.2    +      -       -      +
    247A  PHE*     1.3    62.0    +      -       -      +
    248A  VAL      4.5     2.5    -      -       -      +
    249A  HIS*     3.9    40.8    -      -       +      +
    301A  ASP*     3.7     8.1    -      -       -      +
    424A  ALA*     4.7     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 247 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  ALA*     2.8    18.6    +      -       +      +
    232A  PHE*     3.6    11.2    -      -       -      -
    233A  LEU*     3.6    36.6    -      -       +      -
    245A  HIS*     3.9     2.9    -      +       -      -
    246A  LEU*     1.3    72.6    -      -       -      +
    248A  VAL*     1.3    67.6    +      -       -      +
    300A  ALA*     3.4     0.4    -      -       +      -
    301A  ASP      2.8    44.4    +      -       -      +
    302A  LEU*     4.1    15.7    -      -       +      -
    304A  THR*     3.9    23.3    -      -       +      -
    314A  TYR*     4.0    22.7    -      +       -      -
    366A  LEU*     5.3     2.2    -      -       +      -
    374A  ILE*     4.2    22.9    -      -       +      -
    378A  LYS*     5.8     0.7    -      -       +      -
    424A  ALA*     3.4     6.3    -      -       -      +
    501A  MYR      3.8    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 248 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  PHE*     4.1     6.7    -      -       +      -
    230A  SER*     3.4     1.6    -      -       -      -
    231A  ALA*     3.1    45.5    +      -       +      +
    246A  LEU*     4.5     1.0    -      -       -      +
    247A  PHE*     1.3    82.2    +      -       -      +
    249A  HIS*     1.3    67.8    +      -       -      +
    298A  PHE*     3.5    53.4    -      -       +      -
    299A  TRP      4.7     1.6    -      -       -      +
    300A  ALA*     3.9    17.7    -      -       +      -
    415A  PHE*     4.4     4.9    -      -       +      -
    424A  ALA*     4.2     6.3    -      -       -      -
    501A  MYR      4.0    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 249 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  PHE      3.2     9.0    -      -       -      +
    230A  SER*     4.0    10.5    -      -       -      -
    246A  LEU*     3.9    31.0    -      -       +      +
    248A  VAL*     1.3    80.9    -      -       -      +
    250A  ILE*     1.3    68.5    +      -       -      +
    251A  GLY*     5.3     1.2    +      -       -      -
    298A  PHE*     4.1     4.8    -      -       -      -
    424A  ALA*     4.0    35.3    +      -       +      +
    426A  HIS*     3.2    25.8    +      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 250 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  VAL*     5.0     4.7    -      -       +      -
    226A  MET*     4.2    27.6    -      -       +      +
    227A  LEU      4.7     6.5    -      -       -      +
    228A  GLU*     3.4     5.8    -      -       -      +
    229A  PHE*     2.7    44.0    +      -       +      +
    230A  SER*     5.5     0.2    -      -       -      -
    249A  HIS*     1.3    81.4    -      -       -      +
    251A  GLY*     1.3    65.2    +      -       -      +
    296A  VAL*     4.1    24.2    -      -       +      -
    298A  PHE*     3.7    28.0    -      -       +      -
    413A  TYR*     4.7     1.8    -      -       +      -
    426A  HIS*     4.1    17.7    -      -       +      +
    428A  ILE*     4.4    21.8    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il